One of the members in our club just did that to his TJ yesterday (I helped, sorta) and it turned out great.
His flares had become damaged from trees, so he sanded them down, filled in the gouges with flexible body filler, sanded again, wiped with paper towel, washed with brake cleaner then painted.
He painted them with rattle-can box liner for trucks. Post back in a couple months so I can ask him how well they hold up to the winter driving we have here.
Hello, my name is Vance and I am a Jeepaholic.
Its better to be naked with your friends, than to be clothed with your enemies
Silver 2006 TJ Unlimited
, zombie ready as the daily-driver